An apparatus and a method for controlling a flow control valve for a high-pressure fuel pump include: a pressure sensor for fuel in a delivery pipe; a control unit for controlling an operation of a flow control valve by controlling a current applied to a coil; a power switching unit for supplying or blocking driving power supplied to the flow control valve based on a control signal of the control unit; and a current adjustment unit electrically connected/disconnected with the flow control valve by the power switching unit to reduce a current supplied to the flow control valve when the current adjustment unit is connected with the flow control valve. Therefore, a noise and a vibration by collision between the plunger and the core upon closing the flow control valve may be attenuated by adjusting a current amount applied to the coil.